Link hero ships scratchpad
Hero ships etc.
(n.b. this idea is essentially based on the hero , myth and normal units in Ageof Mythology...)
Hero Ships -> SuperWeapon Ships -> Normal Ships -> Hero Ships
Where normal ships are the fully designable ones that form the majority of your fleets. They are buildable in unlimited quantities (or whatever the limit would otherwise have been), and are totally player designeable. (note that 'player designeble' doesn't mean we shouldn't provide players with 'suggested/auto' designs, if they don't fancy doing it, or simply to provide a benchmark for them to work from.
Ships with a fixed design, quite possibly even with special models and effects, that have some super destructive weapon system. They'd have some pretty serious restrictions one them (e.g. only one per galaxy/ or empire, or at least a huge maintenance and production cost). I'd envisage each of these becoming unlocked as a result of researching a weapon type and building a special building/wonder, and possible some other restrictions. (E.g. death star becomes unlocked when you've researched lasers, can build spinal mounts and the largest ship hull, and build a Death star development facility special building.)
SuperWeapon ships are fairly deadly against normal ships, doing large amounts of damage, or damaging many ships, or causing special problems like disabling ships etc. In other words they punch well above their weight in terms of cost and effectiveness. Controlled space monsters etc would also fall into this category.
Hero Ships Hero ships are much less powerful ships, not necessarily always even more powerful than normal ships, but usually a fair bit. They represent the elite of you forces. Ships with either history and legend behind them, or simply the best crews and captains and the pick of the equipment in the fleet, or both, or mercenary ships led by legendary aliens... etc. Hero ships might generally emerge/be selected from your regular forces who survive combat, their emergence might be dependant on the existance of certain facilities or research projects (e.g. "Fleet Command training program" might need to be researched before hero's could emerge/be elected from Capital Ships, or building a "Fleet headquarter" might allow you to designate a certain number of veteran normal units as hero units. Hero units should have greatly increased maintenance costs.
Their main benefit is that they are very resistant to the effects of SuperWeapon Ships (e.g. if it's a super shield sapping weapon that knocks out normal ship shields completely for 10 time units, it will only knock hero ship shields down by 30% for 3 time units.), and they have bonuses when attacking superweapon ships. (The idea behind this is that having the best and brigthest crews, or exceptional captains etc, or just being plain lucky, they manage to avoid the worst of the effects and develop innovative attack plans quickly.)
Hero ships might well give some bonuses to the ships around them (either due to superior leadership or just the 'inspiration' factor), but generally they will not really be worth their extra cost, except when you come up against superweapon ship, when they'll be worth their weight in gold as the only ships capable of standing up to them with reasonable odds, and avoiding the huge losses you'd usually take in destroying these SuperShips.
One of the main reasons I like this idea is that it allows people to have both fairly large, pretty disposable fleets, and some ships that they concentrate personally on. Your favourite special weapon ship or hero ship could be something to get attached to, and depressed and bitter about when they get detroyed.